Table 6.
List of best candidate genes identified among the overrepresented bulks of reads from resistant RILs and with the best match with transcriptome data of S. aethiopicum. For each gene, the 305_asm scaffold or contig, the matching S. aethiopicum scaffold (from Gramazio et al. [59]), the percentage of homology and a putative gene prediction are indicated.
| Candidate Genes | Query | Scaffold on S. aethiopicum transcriptome | Identities | Predicted Function Based on Domains Analysis Performed via NCBI Platform | Scaffold on S. aethiopicum Pangenome |
|---|---|---|---|---|---|
| RES1 | SMEL_002g157480.1 (Miyatake et al. [20], orthologous of SOLYC02G032200.2 | SAUC48279_TC01 Length = 3745 | 3392/3418 (99%) Strand = +/+ | Encoding a putative TMV resistance protein N-like LOC102604931, transcript variant X2 | scaffold3814_cov65 (978531-977633) lenght:898 strand (+/−) |
| RES2 | C7021905__121_4977 (348 letters) | SAUC67459_TC01 Length = 578 | 348/348 (100%) Strand = +/− | chaperonin | scafold150403_cov62 (904702-904125) lenght:577 strand (+/−) |
| RES3 | C7104747__218_9061 (1767 letters) | SAUC05724_TC02 Length = 1311 | 915/915 (100%) Strand = +/+ | cysteine-rich RLK (RECEPTOR-like protein kinase) 8 | scafold150406_cov62 (122904-121605) lenght:1299 strand (+/−) |
| RES4 | C7123897__247_10432 (1176 letters) | SAUC85719_TC01 Length = 1281 | 194/194(100%) + 807/807(100%) Strand: +/+ | Putative late blight resistance protein homolog R1A-3 | scaffold149207_cov61 (473206-471925) lenght:1281 strand (+/−) |
| RES5 | scaffold131120__543_23320 (630 letters) | SAUC54187_TC01 Length = 581 | 312/312 (100%) Strand: +/+ | scaffold4400_cov64 (319724-320299) lenght:575 strand (+/+) | |
| RES6 | scaffold151247__813_35520 (1935 letters) | SAUC60998_TC03 Length = 2636 | 986/986(100%) + 719/721(99%) Strand = +/+ | scaffold149470_cov62 (278029-278886) lenght:857 strand (+/+) | |
| RES7 | scaffold161031_1035_45870 (1362 letters) | SAUC62185_TC01 Length = 517 | 517/517 (100%) Strand = +/+ | Protein transparent testa 12-like | scaffold149494_cov61 (246517-247031) lenght:514 strand (+/+) |
| RES8 | scaffold4270_1160_51181 (3702 letters) | SAUC68094_TC01 Length = 4264 | 2697/2697(100%) + 974/974 (100%) Strand = +/− | Putative late blight resistance protein homolog R1B-14-like [Solanum lycopersicum] | scaffold872_cov63 (353791-349798) lenght:3993 strand (+/−) |
| RES9 | scaffold160330_1010_44805 (327 letters) | SAUC18225_TC01 Length = 741 | 327/327(100%) Strand = +/− | scaffold149207_cov61 (183171-183700) lenght:529 strand (+/+) | |
| RES10 | scaffold83272__1378_60779 (375 letters) | SAUC44781_TC01 Length = 543 | 364/364(100%) Strand = +/− | scaffold150551_cov61 (32877-32417) lenght:460 strand (+/−) |